Ecosyste.ms: Issues

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GitHub / broadinstitute/picard issues and pull requests

#1729 - Read CIGAR M operator maps off end of reference

Issue - State: closed - Opened by BaylieRW almost 3 years ago - 1 comment

#1724 - GtcToVcf & CreateExtendedIlluminaManifest - support for GRCh38

Issue - State: open - Opened by kew24 about 3 years ago - 4 comments

#1721 - Update CrosscheckFingerprints summary

Pull Request - State: closed - Opened by derekca about 3 years ago - 3 comments

#1720 - Feature request: common flag to disable metrics requiring external dependencies (e.g. R)

Issue - State: open - Opened by matthdsm about 3 years ago - 3 comments
Labels: R-Dependency

#1710 - MergeBamAlignment needlessly requires input BAMs to be sorted by queryname

Issue - State: closed - Opened by freeseek about 3 years ago - 7 comments

#1709 - Picard from Bionconda 2.26 can not read BARCODE_FILE

Issue - State: closed - Opened by crossz about 3 years ago - 4 comments

#1693 - bug report: MergeBamAlignment fails to merge ubam and bam

Issue - State: closed - Opened by fardokhtsadat over 3 years ago - 2 comments

#1692 - Can't find picard-tools-x.y.z.zip at Latest Release project page.

Issue - State: closed - Opened by rsharris over 3 years ago - 4 comments

#1691 - BedToIntervalList error

Issue - State: closed - Opened by xiucz over 3 years ago - 2 comments

#1689 - Aligned record iterator (...) is behind the unmapped reads

Issue - State: closed - Opened by marctormo over 3 years ago - 3 comments

#1681 - Picard FixVcfHeader possible bug

Issue - State: closed - Opened by NTNguyen13 over 3 years ago - 1 comment

#1657 - How you can keep RX barcode in uBAM after FastqToSam?

Issue - State: closed - Opened by MatteoZam over 3 years ago - 1 comment

#1652 - Markduplicates with UMI in GATK pipeline, which is the correct approach?

Issue - State: open - Opened by MatteoZam over 3 years ago - 3 comments

#1644 - installation instructions for picard version 1.43

Issue - State: closed - Opened by JamalEH over 3 years ago

#1632 - How can I use CollectRnaSeqMetrics with an ENSEMBL annotated BAM file?

Issue - State: closed - Opened by rpauly over 3 years ago - 1 comment

#1631 - CollectVariantCallingMetrics throws NullPointerException

Issue - State: closed - Opened by jezkoski over 3 years ago - 2 comments

#1620 - Allow CollectRnaSeqMetrics to take in a GTF file

Pull Request - State: closed - Opened by sophiacrennan almost 4 years ago - 2 comments
Labels: On Hold

#1605 - CollectHsMetrics BAIT_INTERVALS and TARGET_INTERVALS need better definitions

Issue - State: open - Opened by alanhoyle almost 4 years ago - 1 comment

#1604 - getting error in MarkDuplicates

Issue - State: closed - Opened by shanmugavadivelps almost 4 years ago - 2 comments

#1588 - Add usage instructions to dockerhub

Issue - State: open - Opened by moldach almost 4 years ago - 1 comment

#1580 - Include common (engine-level) args in help output by default.

Pull Request - State: closed - Opened by cmnbroad about 4 years ago - 6 comments

#1565 - Error on fixing ReadGroups

Issue - State: closed - Opened by elbakrifz about 4 years ago - 1 comment

#1552 - LiftoverVCF does not liftover INFO/END for SVs

Issue - State: open - Opened by cmnbroad about 4 years ago - 12 comments

#1552 - LiftoverVCF does not liftover INFO/END for SVs

Issue - State: open - Opened by cmnbroad about 4 years ago - 9 comments

#1549 - Identify Contaminant Background Option and LoH handling

Pull Request - State: closed - Opened by kachulis about 4 years ago - 3 comments
Labels: On Hold

#1524 - Long references (>2^29)

Issue - State: open - Opened by SergejN over 4 years ago - 4 comments

#1496 - Bugfix for IdentifyContamiant + small improvements to Fingerprinting

Pull Request - State: closed - Opened by yfarjoun over 4 years ago - 4 comments

#1478 - Add the EXT argument to CollectSamErrorMetrics.

Pull Request - State: closed - Opened by nh13 over 4 years ago
Labels: Waiting For Revisions

#1476 - Make the VCF option in CollectSamErrorMetrics optional.

Pull Request - State: closed - Opened by nh13 over 4 years ago
Labels: Waiting For Revisions

#1474 - #Error:Heap-Memory Issues

Issue - State: closed - Opened by Rohit-Satyam over 4 years ago - 3 comments

#1473 - Intensity Test Data (BCL) Origin

Issue - State: closed - Opened by emretaylanduman over 4 years ago

#1472 - BuildBamIndex should support index creation for CRAM

Issue - State: open - Opened by cmnbroad over 4 years ago

#1459 - UmiAwareMarkDuplicatesWithMateCigar random error

Issue - State: closed - Opened by sybrohee over 4 years ago - 19 comments

#1452 - Liftover Issue for HGDP panel

Issue - State: closed - Opened by Anahit19 over 4 years ago - 1 comment

#1441 - MarkDuplicates Missing Optical Duplicates

Issue - State: open - Opened by whitwham almost 5 years ago - 7 comments

#1433 - Stop removing periods from the end of output names

Pull Request - State: closed - Opened by tlangs almost 5 years ago - 4 comments

#1431 - CollectInsertSizeMetrics Error

Issue - State: closed - Opened by nicolasalexandre21 almost 5 years ago - 2 comments

#1418 - liftover failed to recognize the swapped alleles

Issue - State: closed - Opened by chenwenan almost 5 years ago - 6 comments

#1409 - CollectWgsMetrics per chromosome merge

Issue - State: closed - Opened by Stikus almost 5 years ago - 3 comments

#1360 - Picard 2.20.3 markduplicates error

Issue - State: closed - Opened by willright28 about 5 years ago - 7 comments

#1355 - MarkDuplicates Code

Issue - State: closed - Opened by fxjonas about 5 years ago

#1352 - MarkDuplicates CRAM output support?

Issue - State: closed - Opened by simoncchu over 5 years ago - 3 comments

#1340 - Update CollectSamErrorMetrics.java

Pull Request - State: closed - Opened by nh13 over 5 years ago - 6 comments
Labels: Waiting For Revisions

#1340 - Update CollectSamErrorMetrics.java

Pull Request - State: closed - Opened by nh13 over 5 years ago - 6 comments
Labels: Waiting For Revisions

#1330 - Meaning of CollectRnaSeqMetrics histogram?

Issue - State: open - Opened by nicolerg over 5 years ago - 4 comments
Labels: docs

#1276 - add R as a pre-requisite

Issue - State: open - Opened by igordot over 5 years ago
Labels: R-Dependency

#1253 - queryname sorted BAM Markduplication ran a long time without any output

Issue - State: closed - Opened by biozzq almost 6 years ago - 4 comments

#1252 - pixel distance for MarkDuplicates Novaseq flow-cells

Issue - State: closed - Opened by splaisan almost 6 years ago - 6 comments

#1227 - IlluminaBasecallsToFastq does not write unassigned reads to file

Issue - State: closed - Opened by rithy8 about 6 years ago - 1 comment

#1159 - Error in MergeBamAlignment

Issue - State: closed - Opened by alrafaykhan over 6 years ago - 5 comments

#1081 - How to use USE_SEQUENTIAL_FASTQS option

Issue - State: closed - Opened by romagnolid over 6 years ago

#1008 - RevertSam does not accept /dev/stdin and should have a better error message

Issue - State: open - Opened by nh13 almost 7 years ago - 8 comments
Labels: stdin/stdout

#915 - Accept piped input FastqToSam

Issue - State: closed - Opened by yesimon about 7 years ago - 7 comments

#831 - Add auxiliary baits and targets to BaitDesigner.

Pull Request - State: closed - Opened by nh13 over 7 years ago - 6 comments

#801 - Is it possible to make Picard MarkDuplicates to support multiple threads?

Issue - State: closed - Opened by liugui over 7 years ago - 7 comments

#630 - Picard cannot write to stdout

Issue - State: open - Opened by nh13 about 8 years ago - 2 comments
Labels: bug, stdin/stdout

#507 - UpdateVcfSequenceDictionary should handle stdin and stdout gracefully

Issue - State: open - Opened by nh13 over 8 years ago - 25 comments
Labels: bug, secon, cleanup